doc fixes

pypeit · Aug 15, 2023 · 270f886 · 270f886
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diff --git a/doc/calibrations/calibrations.rst b/doc/calibrations/calibrations.rst
@@ -1,4 +1,6 @@
 
+.. include:: ../include/links.rst
+
 .. _calibrations:
 
 ============

diff --git a/doc/calibrations/wave_calib.rst b/doc/calibrations/wave_calib.rst
@@ -270,13 +270,19 @@ grating equation.
 
 In general, the approach is:
 
-    1. Identify the arc lines in each order
-    2. Fit the arc lines in each order to a polynomial, individually
-    3. Fit a 2D solution to the lines using the order number as a basis
-    4. Reject orders where the RMS of the fit (measured in binned pixels) exceeds ``rms_threshold``
-    5. Attempt to recover the missing orders using the 2D fit and 
-      a higher RMS threshold
-    6. Refit the 2D solution
+    #. Identify the arc lines in each order
+
+    #. Fit the arc lines in each order to a polynomial, individually
+
+    #. Fit a 2D solution to the lines using the order number as a basis
+
+    #. Reject orders where the RMS of the fit (measured in binned pixels)
+       exceeds ``rms_threshold``
+
+    #. Attempt to recover the missing orders using the 2D fit and a higher RMS
+       threshold
+
+    #. Refit the 2D solution
 
 One should always inspect the outputs, especially the 2D solution
 (global and orders).  One may then need to modify the ``rms_threshold``

diff --git a/doc/include/gemini_gnirs_echelle_A_corrected.pypeit.rst b/doc/include/gemini_gnirs_echelle_A_corrected.pypeit.rst
@@ -6,10 +6,10 @@
     # User-defined execution parameters
     [rdx]
     spectrograph = gemini_gnirs_echelle
-    [calibrations]
-     [[wavelengths]]
-        rms_threshold = 0.8, 0.4, 0.8, 0.8, 0.5, 0.9
-        sigdetect = 5.,5.,6.,6.,5.,7.
+    #[calibrations]
+    # [[wavelengths]]
+    #    rms_threshold = 0.8, 0.4, 0.8, 0.8, 0.5, 0.9
+    #    sigdetect = 5.,5.,6.,6.,5.,7.
     
     # Setup
     setup read

diff --git a/doc/pypeit_par.rst b/doc/pypeit_par.rst
diff --git a/doc/spectrographs/spectrographs.rst b/doc/spectrographs/spectrographs.rst
@@ -38,6 +38,7 @@ instrument-specific details for running PypeIt.
    gemini_gnirs
    gtc_osiris
    deimos
+   keck_hires
    keck_kcwi
    lris
    keck_nires

diff --git a/doc/spectrographs/xshooter.rst b/doc/spectrographs/xshooter.rst
@@ -30,7 +30,7 @@ FWHM
 
 For the UVB or the VIS, you may turn off measuring the FWHM (in units
 of binned pixdels) from the arc lines
-by adding this to your :doc:`pypeit_file`:
+by adding this to your :ref:`pypeit_file`:
 
 
 .. code-block:: ini
@@ -46,7 +46,7 @@ RMS
 ---
 
 Another option is to increase the RMS threshold for a good solution.
-This may be done in the :doc:`pypeit_file` as well:
+This may be done in the :ref:`pypeit_file` as well:
 
 .. code-block:: ini
 
@@ -56,5 +56,5 @@ This may be done in the :doc:`pypeit_file` as well:
 
 
 Note that this is scaled by the ratio of the measured FWHM value
-to the default value.  See :ref:`_wvcalib-echelle` for
+to the default value.  See :ref:`wvcalib-echelle` for
 further details.
diff --git a/pypeit/core/wavecal/patterns.py b/pypeit/core/wavecal/patterns.py
@@ -1,4 +1,6 @@
 """ Module for finding patterns in arc line spectra
+
+.. include:: ../include/links.rst
 """
 import numpy as np
 import scipy.ndimage

diff --git a/pypeit/wavecalib.py b/pypeit/wavecalib.py
@@ -862,23 +862,25 @@ def echelle_2dfit(self, wv_calib, debug=False, skip_QA=False):
         Primarily a wrapper for :func:`pypeit.core.arc.fit2darc`,
         using data unpacked from the ``wv_calib`` dictionary.
 
-        Args:
-            wv_calib (:class:`pypeit.wavecalib.WaveCalib`):
-                Wavelength calibration object
-            debug (:obj:`bool`, optional):
-                Show debugging info
-            skip_QA (:obj:`bool`, optional):
-                Flag to skip construction of the nominal QA plots.
+        Parameters
+        ----------
+        wv_calib : :class:`pypeit.wavecalib.WaveCalib`
+            Wavelength calibration object
+        debug : :obj:`bool`, optional
+            Show debugging info
+        skip_QA : :obj:`bool`, optional
+            Flag to skip construction of the nominal QA plots.
 
-        Returns:
-            tuple: 
-                - ``fit2ds``: a list of :class:`pypeit.fitting.PypeItFit`: objects 
-                containing information from 2-d fit.  Frequently a list of 1 fit.  
-                The main exception is for a mosaic when one sets ``echelle_separate_2d=True``.
-    
-                - ``dets``: a list of integers for the detector numbers.
-
-                - ``order_dets``: a list of integer lists providing list of the orders.
+        Returns
+        -------
+        fit2ds : list of :class:`pypeit.fitting.PypeItFit`
+            Contains information from 2-d fit.  Frequently a list of 1 fit.  The
+            main exception is for a mosaic when one sets
+            ``echelle_separate_2d=True``.
+        dets : list
+            List of integers for the detector numbers.
+        save_order_dets: list
+            List of integer lists providing list of the orders.
         """
         if self.spectrograph.pypeline != 'Echelle':
             msgs.error('Cannot execute echelle_2dfit for a non-echelle spectrograph.')